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ABC.RAP (version 0.9.0)
Array Based CpG Region Analysis Pipeline
Description
It aims to identify candidate genes that are “differentially methylated” between cases and controls. It applies Student’s t-test and delta beta analysis to identify candidate genes containing multiple “CpG sites”.
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Version
Version
0.9.0
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Install
install.packages('ABC.RAP')
Monthly Downloads
330
Version
0.9.0
License
GPL-3
Maintainer
Abdulmonem Alsaleh
Last Published
October 20th, 2016
Functions in ABC.RAP (0.9.0)
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plot_data
Overview description of the DNA methylation pattern for cases and controls
ttest_data
applying t-test analysis
process.ABC.RAP
An automated analysis applying all ABC.RAP functions in one script
test_data
test dataset of 450k DNA methylation
CpG_hits
Identifying genes for which multiple CpG sites show significant methylation difference
annotate_data
Annotating the filtered probes
overlap_data
Overlapping Student's t-test and delta beta results
filter_data
Filtering DNA methylation 450k non_specific probes
plot_gene
Plotting and exporting methylation profile for candidate genes
annotation_file
annotation file for the 450k probes
delta_beta_data
Applying delta beta analysis to calculate the difference between cases and controls
nonspecific_probes
450k DNA methylation non specific probes
plot_candidate_genes
Plotting highly different and significant probes annotated by their corresponding gene names